/EXTERNAL McGill EMC/variants/K006189_1_lane_gembs
BACK
SAMPLE K006189_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1145565905 |
702190171 |
61.30 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1145565905 |
100% |
1134303257 |
99.02 % |
11262648 |
0.98 % |
| |
|
|
|
|
|
|
| Passed |
703789938 |
61.44 % |
700161425 |
61.73 % |
3628513 |
0.52 % |
| Filtered |
441775967 |
38.56 % |
434141832 |
38.27 % |
7634135 |
1.08 % |
| |
|
|
|
|
|
|
| q20 |
407477068 |
92.24 % |
405823653 |
93.48 % |
1653415 |
21.66 % |
| q20,qd2 |
14394905 |
3.26 % |
8844657 |
2.04 % |
5550248 |
72.70 % |
| q20,mq40 |
12426849 |
2.81 % |
12328114 |
2.84 % |
98735 |
1.29 % |
| q20,qd2,mq40 |
3116059 |
0.71 % |
2997210 |
0.69 % |
118849 |
1.56 % |
| qd2 |
2632830 |
0.60 % |
2576524 |
0.59 % |
56306 |
0.74 % |
| mq40 |
1685169 |
0.38 % |
1537569 |
0.35 % |
147600 |
1.93 % |
| qd2,mq40 |
41688 |
0.01 % |
34105 |
0.01 % |
7583 |
0.10 % |
| qd2,fs60,mq40 |
624 |
0.00 % |
0 |
0.00 % |
624 |
0.01 % |
| fs60,mq40 |
234 |
0.00 % |
0 |
0.00 % |
234 |
0.00 % |
| qd2,fs60 |
230 |
0.00 % |
0 |
0.00 % |
230 |
0.00 % |
| fs60 |
191 |
0.00 % |
0 |
0.00 % |
191 |
0.00 % |
| q20,qd2,fs60 |
74 |
0.00 % |
0 |
0.00 % |
74 |
0.00 % |
| q20,qd2,fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
3687052 |
28.46 % |
| Transition |
G>A |
All |
1051215 |
8.11 % |
| Transition |
T>C |
All |
3286504 |
25.36 % |
| Transition |
C>T |
All |
1086602 |
8.39 % |
| Transversion |
A>C |
All |
224420 |
1.73 % |
| Transversion |
C>A |
All |
1113555 |
8.59 % |
| Transversion |
T>G |
All |
246924 |
1.91 % |
| Transversion |
G>T |
All |
1090085 |
8.41 % |
| Transversion |
A>T |
All |
344159 |
2.66 % |
| Transversion |
T>A |
All |
356662 |
2.75 % |
| Transversion |
C>G |
All |
243168 |
1.88 % |
| Transversion |
G>C |
All |
226990 |
1.75 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
466297 |
16.43 % |
| Transition |
G>A |
Passed |
461429 |
16.26 % |
| Transition |
T>C |
Passed |
467900 |
16.49 % |
| Transition |
C>T |
Passed |
470840 |
16.59 % |
| Transversion |
A>C |
Passed |
119527 |
4.21 % |
| Transversion |
C>A |
Passed |
132770 |
4.68 % |
| Transversion |
T>G |
Passed |
119709 |
4.22 % |
| Transversion |
G>T |
Passed |
131065 |
4.62 % |
| Transversion |
A>T |
Passed |
113047 |
3.98 % |
| Transversion |
T>A |
Passed |
112885 |
3.98 % |
| Transversion |
C>G |
Passed |
121115 |
4.27 % |
| Transversion |
G>C |
Passed |
121484 |
4.28 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
2.37 |
9111373 |
3845963 |
| Passed |
1.92 |
1866466 |
971602 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |